Pittsburgh Supercomputing Center’s MARC Program Builds Bioinformatics Expertise at Minority Universities
For more than 10 years PSC’s Minority Access to Research Careers program has addressed a disparity identified in 2011 as an NIH priority.
PITTSBURGH, July 5, 2012 — A training program of the National Resource for Biomedical Supercomputing (NRBSC) at the Pittsburgh Supercomputing Center (PSC) has taken a unique pro-active role toward filling the gap in scientific training at minority-serving institutions (MSIs). Since 2001, with funding from NIH’s National Institute of General Medical Sciences, PSC’s MARC (Minority Access to Research Careers) program has evolved from providing individual training in what was at first a newly emerging discipline, bioinformatics, to a focus on the development of curricula and research programs at partner universities.
“We’ve implemented a multi-disciplinary course in sequence-based bioinformatics at more than 10 universities,” says PSC scientist Hugh Nicholas, who directs the MARC program. As of 2011, with renewal of the program from NIH for five years, the effort of Nicholas and his PSC colleagues, Troy Wymore and Alex Ropelewski, in working with five partner MSIs — North Carolina AT & T; University of Puerto Rico, Mayaguez; Johnson C. Smith University; Tennessee State University; and Jackson State University — is to build a concentration or minor in bioinformatics. This expanded outreach reflects dramatic changes in bioinformatics, a field that over the last few years has exploded, because of powerful new sequencing technologies, with data to be analyzed and opportunities to do important research.
“The program has shifted direction,” says Ricardo González, a professor at the University of Puerto Rico, School of Medicine, and co-principal investigator with Nicholas in PSC’s MARC program. “We’ve become good enough to establish bioinformatics programs or tracks at these universities and to provide a solid foundation for their faculty and students to carry out research in this field.”
Along with workshops at PSC, the MARC staff travels to partner MSIs to offer intensive on-site workshops. The program also provides a model curriculum for bioinformatics, with course materials in related aspects of biology, computational science and mathematics, and offers teaching assistance for newly established courses. “At each campus with which we’ve partnered,” says Nicholas, “we’ve trained people who are now capable of teaching a basic bioinformatics course.”
Many peer-reviewed papers have already resulted from PSC’s program, notes González, work that is especially important, he observes, in light of a 2011 NIH study (Science, August 19, 2011) finding that black scientists were a third less likely than white counterparts to get a research project funded. “The PSC program has been addressing the uneven playing field that affects black researchers for 10 years.”
González and faculty liaisons from the partner MSIs gathered at PSC on June 28 to assess progress as PSC’s program concluded its 2012 Summer Institute. This two-week workshop, which PSC has hosted since 2003, trains graduate students, who can use bioinformatics tools to complete dissertation research, and faculty who plan to establish an introductory bioinformatics course at their home institution. This year 17 faculty and graduate students from eight universities attended.
In addition to the Summer Institute, the program also offers a seven-week research internship on-site at PSC, with 10 participants this year. These internships build connections for young scientists with resources at two major research universities, Carnegie Mellon and the University of Pittsburgh, and have often led to published research — including a project in sequencing of bacteriophage genes by one of the program’s first interns, from Howard University: http://www.psc.edu/science/2004/dobbins/
Through the MARC program, partner MSIs have access to PSC resources, including BioU, a computing cluster used for bioinformatics teaching, and PSC’s Blacklight an SGI® Altix® UV1000 system that is the largest shared-memory systems in the world, and is a resource of the NSF’s XSEDE (Extreme Science and Engineering Discovery Environment) cyberinfrastructure program.
XSEDE access is especially useful in bioinformatics as “next generation” sequencing instruments produce skyrocketing quantities of genomics data and make possible many new avenues of research. Tools such as Penn State’s Galaxy — an open, web-based platform used for data intensive bioinformatics workflows — help to reduce the steep learning curve. “Galaxy eliminates a lot of the complexity of getting started in this field,” says Nicholas. “It has become the preferred way to perform bioinformatics analyses for both research and teaching.”
PSC has recently added a high-speed network link to the main Galaxy portal at Penn State. See: http://psc.edu/index.php/newscenter/71-2012press/670-pittsburgh-supercomputing-center-provides-direct-link-from-galaxy-to-the-xsede-backbone
PSC’s workshops in the techniques of sequence analysis began in 1989 in response to the development of computing technologies as powerful tools for biological research. “The traditional manner of biological training has been laboratory focused,” notes Nicholas, an expert in genetic sequence analysis, “and it’s a distinct shift in training to incorporate computational techniques into the biologist’s repertoire.”
Having emerged over the last decade as a major thrust of the life sciences, bioinformatics marries information science and statistics with biology. “Computational tools,” says Nicholas, “allow researchers to understand biological systems like never before. But researchers need to learn about these new and rapidly improving tools.”
The MARC program sprang from a collaboration with the University of Puerto Rico School of Medicine, after González took a series of PSC workshops in the late 1990s. He invited Nicholas and other PSC scientists to provide their training on-site to his colleagues in San Juan and encouraged the PSC scientists to seek funding under NIH’s MARC initiative.
“This is one of the longest funded training grants in NIH,” says González, “and it is strong because of PSC’s ability to build bridges with scientists at historically black universities and MSIs.” Among other MARC programs, PSC’s is unique at being situated external to an MSI and in its focus on building and sustaining curricula and research programs at partner MSIs.
The current advisory committee for PSC’s MARC program: Charles L. Brooks III, University of Michigan; Dannie Durand, Carnegie Mellon University; Daniel M. Gusfield, University of California; Michael Gribskov, Purdue University, and Stephen B. Aley, University of Texas at El Paso.
About PSC’s MARC program:
About NRBSC: http://www.nrbsc.org